X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureRenderer.java;h=b88a1dcd750b89a0e6fdb2a1bb92dffe6e6c6a2f;hb=c9e79462a42264c560a828808934a3a156c39d0c;hp=adfa51850509cfc970f970b39201978cdef02828;hpb=42fe80f86baa12e456936ff789ea5f0f8f03c574;p=jalview.git diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java old mode 100755 new mode 100644 index adfa518..b88a1dc --- a/src/jalview/appletgui/FeatureRenderer.java +++ b/src/jalview/appletgui/FeatureRenderer.java @@ -1,463 +1,464 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import java.util.*; - -import java.awt.*; - -import jalview.datamodel.*; +import jalview.api.FeatureColourI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; +import jalview.io.FeaturesFile; +import jalview.schemes.FeatureColour; +import jalview.util.ColorUtils; +import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; + +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Choice; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.Graphics; +import java.awt.GridLayout; +import java.awt.Label; +import java.awt.Panel; +import java.awt.ScrollPane; +import java.awt.TextArea; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; +import java.util.Hashtable; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class FeatureRenderer +public class FeatureRenderer extends + jalview.renderer.seqfeatures.FeatureRenderer { - AlignViewport av; - - Hashtable featureColours = new Hashtable(); - - // A higher level for grouping features of a - // particular type - Hashtable featureGroups = null; // Holds web links for feature groups and feature types // in the form label|link Hashtable featureLinks = null; - // This is actually an Integer held in the hashtable, - // Retrieved using the key feature type - Object currentColour; - - String[] renderOrder; - - FontMetrics fm; - int charOffset; - - float transparency = 1f; - - TransparencySetter transparencySetter = null; - /** * Creates a new FeatureRenderer object. - * - * @param av DOCUMENT ME! + * + * @param av */ - public FeatureRenderer(AlignViewport av) + public FeatureRenderer(AlignmentViewport av) { - this.av = av; + super(av); - if (!System.getProperty("java.version").startsWith("1.1")) - { - transparencySetter = new TransparencySetter(); - } } - public void transferSettings(FeatureRenderer fr) - { - renderOrder = fr.renderOrder; - featureGroups = fr.featureGroups; - featureColours = fr.featureColours; - transparency = fr.transparency; - } - - public Color findFeatureColour(Color initialCol, SequenceI seq, int i) - { - overview = true; - if (!av.showSequenceFeatures) - { - return initialCol; - } + static String lastFeatureAdded; - lastSequence = seq; - sequenceFeatures = lastSequence.getSequenceFeatures(); - if (sequenceFeatures == null) - { - return initialCol; - } + static String lastFeatureGroupAdded; - sfSize = sequenceFeatures.length; + static String lastDescriptionAdded; - if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i))) - { - return Color.white; - } + int featureIndex = 0; - currentColour = null; + boolean deleteFeature = false; - drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1); + FeatureColourPanel colourPanel; - if (currentColour == null) - { - return initialCol; - } - - return new Color( ( (Integer) currentColour).intValue()); - } + class FeatureColourPanel extends Panel + { + String label = ""; - /** - * This is used by the Molecule Viewer to get the accurate colour - * of the rendered sequence - */ - boolean overview = false; + private Color maxCol; - int white = Color.white.getRGB(); - public int findFeatureColour(int initialCol, int seqIndex, int column) - { - if (!av.showSequenceFeatures) - { - return initialCol; - } + private boolean isColourByLabel, isGcol; - if (seqIndex != lastSequenceIndex) + /** + * render a feature style in the amend feature dialog box + */ + public void updateColor(FeatureColourI newcol) { - lastSequence = av.alignment.getSequenceAt(seqIndex); - lastSequenceIndex = seqIndex; - sequenceFeatures = lastSequence.getSequenceFeatures(); - if (sequenceFeatures == null) + Color bg = null; + String vlabel = ""; + if (newcol.isSimpleColour()) { - return initialCol; + bg = newcol.getColour(); + setBackground(bg); } + else + { + if (newcol.isAboveThreshold()) + { + vlabel += " (>)"; + } + else if (newcol.isBelowThreshold()) + { + vlabel += " (<)"; + } - sfSize = sequenceFeatures.length; + if (isColourByLabel = newcol.isColourByLabel()) + { + setBackground(bg = Color.white); + vlabel += " (by Label)"; + } + else + { + setBackground(bg = newcol.getMinColour()); + maxCol = newcol.getMaxColour(); + } + } + label = vlabel; + setBackground(bg); + repaint(); } - if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column))) + FeatureColourPanel() { - return Color.white.getRGB(); + super(null); } - currentColour = null; - - drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1); - - if (currentColour == null) + @Override + public void paint(Graphics g) { - return initialCol; + Dimension d = getSize(); + if (isGcol) + { + if (isColourByLabel) + { + g.setColor(Color.white); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + g.setColor(Color.black); + Font f = new Font("Verdana", Font.PLAIN, 10); + g.setFont(f); + g.drawString(MessageManager.getString("label.label"), 0, 0); + } + else + { + g.setColor(maxCol); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + + } + } } - return ( (Integer) currentColour).intValue(); } - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - * @param seq DOCUMENT ME! - * @param sg DOCUMENT ME! - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - * @param x1 DOCUMENT ME! - * @param y1 DOCUMENT ME! - * @param width DOCUMENT ME! - * @param height DOCUMENT ME! - */ - // String type; - // SequenceFeature sf; - int lastSequenceIndex = -1; - SequenceI lastSequence; - SequenceFeature[] sequenceFeatures; - int sfSize, sfindex, spos, epos; - - public void drawSequence(Graphics g, SequenceI seq, - int start, int end, int y1) + boolean amendFeatures(final SequenceI[] sequences, + final SequenceFeature[] features, boolean newFeatures, + final AlignmentPanel ap) { - if (seq.getSequenceFeatures() == null - || seq.getSequenceFeatures().length == 0) + Panel bigPanel = new Panel(new BorderLayout()); + final TextField name = new TextField(16); + final TextField source = new TextField(16); + final TextArea description = new TextArea(3, 35); + final TextField start = new TextField(8); + final TextField end = new TextField(8); + final Choice overlaps; + Button deleteButton = new Button("Delete"); + deleteFeature = false; + + colourPanel = new FeatureColourPanel(); + colourPanel.setSize(110, 15); + final FeatureRenderer fr = this; + + Panel panel = new Panel(new GridLayout(3, 1)); + + featureIndex = 0; // feature to be amended. + Panel tmp; + + // ///////////////////////////////////// + // /MULTIPLE FEATURES AT SELECTED RESIDUE + if (!newFeatures && features.length > 1) { - return; - } + panel = new Panel(new GridLayout(4, 1)); + tmp = new Panel(); + tmp.add(new Label("Select Feature: ")); + overlaps = new Choice(); + for (int i = 0; i < features.length; i++) + { + String item = features[i].getType() + "/" + features[i].getBegin() + + "-" + features[i].getEnd(); - if (transparencySetter != null && g != null) - { - transparencySetter.setTransparency(g, transparency); - } - - if (lastSequence == null || seq != lastSequence || sequenceFeatures!=seq.getSequenceFeatures()) - { - lastSequence = seq; - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } + if (features[i].getFeatureGroup() != null) + { + item += " (" + features[i].getFeatureGroup() + ")"; + } - if (av.featuresDisplayed == null || renderOrder == null) - { - findAllFeatures(); - if (av.featuresDisplayed.size() < 1) - { - return; + overlaps.addItem(item); } - sequenceFeatures = seq.getSequenceFeatures(); - sfSize = sequenceFeatures.length; - } - if (!overview) - { - spos = lastSequence.findPosition(start); - epos = lastSequence.findPosition(end); - if (g != null) - { - fm = g.getFontMetrics(); - } - } - String type; - for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++) - { - type = renderOrder[renderIndex]; - if (!av.featuresDisplayed.containsKey(type)) - { - continue; - } + tmp.add(overlaps); - // loop through all features in sequence to find - // current feature to render - for (sfindex = 0; sfindex < sfSize; sfindex++) + overlaps.addItemListener(new java.awt.event.ItemListener() { - if (!sequenceFeatures[sfindex].type.equals(type)) + @Override + public void itemStateChanged(java.awt.event.ItemEvent e) { - continue; - } + int index = overlaps.getSelectedIndex(); + if (index != -1) + { + featureIndex = index; + name.setText(features[index].getType()); + description.setText(features[index].getDescription()); + source.setText(features[index].getFeatureGroup()); + start.setText(features[index].getBegin() + ""); + end.setText(features[index].getEnd() + ""); - if (featureGroups != null - && sequenceFeatures[sfindex].featureGroup != null - && - featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup) - && - ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex]. - featureGroup)). - booleanValue()) - { - continue; - } + SearchResultsI highlight = new SearchResults(); + highlight.addResult(sequences[0], features[index].getBegin(), + features[index].getEnd()); - if (!overview && (sequenceFeatures[sfindex].getBegin() > epos - || sequenceFeatures[sfindex].getEnd() < spos)) - { - continue; - } + ap.seqPanel.seqCanvas.highlightSearchResults(highlight); - if (overview) - { - if (sequenceFeatures[sfindex].begin <= start && - sequenceFeatures[sfindex].end >= start) + } + FeatureColourI col = getFeatureStyle(name.getText()); + if (col == null) { - currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex]. - type); + Color generatedColour = ColorUtils + .createColourFromName(name.getText()); + col = new FeatureColour(generatedColour); } + colourPanel.updateColor(col); } - else if (sequenceFeatures[sfindex].type.equals("disulfide bond")) - { + }); + + panel.add(tmp); + } + // //////// + // //////////////////////////////////// - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - new Color( ( (Integer) av.featuresDisplayed.get( - sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - new Color( ( (Integer) av.featuresDisplayed.get( - sequenceFeatures[sfindex].type)).intValue()), - start, end, y1); + tmp = new Panel(); + panel.add(tmp); + tmp.add(new Label(MessageManager.getString("label.name:"), Label.RIGHT)); + tmp.add(name); - } - else - { - renderFeature(g, seq, - seq.findIndex(sequenceFeatures[sfindex].begin) - 1, - seq.findIndex(sequenceFeatures[sfindex].end) - 1, - getColour(sequenceFeatures[sfindex].type), - start, end, y1); - } + tmp = new Panel(); + panel.add(tmp); + tmp.add(new Label(MessageManager.getString("label.group:"), Label.RIGHT)); + tmp.add(source); - } - } + tmp = new Panel(); + panel.add(tmp); + tmp.add(new Label(MessageManager.getString("label.colour"), Label.RIGHT)); + tmp.add(colourPanel); + + bigPanel.add(panel, BorderLayout.NORTH); + + panel = new Panel(); + panel.add(new Label(MessageManager.getString("label.description:"), + Label.RIGHT)); + panel.add(new ScrollPane().add(description)); - if (transparencySetter != null && g != null) + if (!newFeatures) { - transparencySetter.setTransparency(g, 1.0f); + bigPanel.add(panel, BorderLayout.SOUTH); + + panel = new Panel(); + panel.add(new Label(MessageManager.getString("label.start"), + Label.RIGHT)); + panel.add(start); + panel.add(new Label(MessageManager.getString("label.end"), + Label.RIGHT)); + panel.add(end); + bigPanel.add(panel, BorderLayout.CENTER); + } + else + { + bigPanel.add(panel, BorderLayout.CENTER); } - } - - char s; - int i; - void renderFeature(Graphics g, SequenceI seq, - int fstart, int fend, Color featureColour, int start, - int end, int y1) - { - if ( ( (fstart <= end) && (fend >= start))) + if (lastFeatureAdded == null) { - if (fstart < start) - { // fix for if the feature we have starts before the sequence start, - fstart = start; // but the feature end is still valid!! + if (features[0].type != null) + { + lastFeatureAdded = features[0].type; } - - if (fend >= end) + else { - fend = end; + lastFeatureAdded = "feature_1"; } + } - for (i = fstart; i <= fend; i++) + if (lastFeatureGroupAdded == null) + { + if (features[0].featureGroup != null) { - s = seq.getCharAt(i); + lastFeatureGroupAdded = features[0].featureGroup; + } + else + { + lastFeatureAdded = "Jalview"; + } + } - if (jalview.util.Comparison.isGap(s)) - { - continue; - } + String title = newFeatures ? MessageManager + .getString("label.create_new_sequence_features") + : MessageManager.formatMessage("label.amend_delete_features", + new String[] { sequences[0].getName() }); - g.setColor(featureColour); + final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385, + 240); - g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight); + dialog.setMainPanel(bigPanel); - if (!av.validCharWidth) + if (newFeatures) + { + name.setText(lastFeatureAdded); + source.setText(lastFeatureGroupAdded); + } + else + { + dialog.ok.setLabel(MessageManager.getString("label.amend")); + dialog.buttonPanel.add(deleteButton, 1); + deleteButton.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) { - continue; + deleteFeature = true; + dialog.setVisible(false); } - - g.setColor(Color.white); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - g.drawString(String.valueOf(s), - charOffset + (av.charWidth * (i - start)), - (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5; - - } + }); + name.setText(features[0].getType()); + source.setText(features[0].getFeatureGroup()); } - } - void findAllFeatures() - { - jalview.schemes.UserColourScheme ucs = new - jalview.schemes.UserColourScheme(); - - av.featuresDisplayed = new Hashtable(); - Vector allfeatures = new Vector(); - for (int i = 0; i < av.alignment.getHeight(); i++) + start.setText(features[0].getBegin() + ""); + end.setText(features[0].getEnd() + ""); + description.setText(features[0].getDescription()); + // lookup (or generate) the feature colour + FeatureColourI fcol = getFeatureStyle(name.getText()); + // simply display the feature color in a box + colourPanel.updateColor(fcol); + dialog.setResizable(true); + // TODO: render the graduated color in the box. + colourPanel.addMouseListener(new MouseAdapter() { - SequenceFeature[] features = av.alignment.getSequenceAt(i). - getSequenceFeatures(); - - if (features == null) - { - continue; - } - - int index = 0; - while (index < features.length) + @Override + public void mousePressed(MouseEvent evt) { - if (!av.featuresDisplayed.containsKey(features[index].getType())) + if (!colourPanel.isGcol) { - if (getColour(features[index].getType()) == null) - { - featureColours.put(features[index].getType(), - ucs.createColourFromName(features[index]. - getType())); - } - - av.featuresDisplayed.put(features[index].getType(), - new Integer(getColour(features[index]. - getType()).getRGB())); - allfeatures.addElement(features[index].getType()); + new UserDefinedColours(fr, ap.alignFrame); + } + else + { + new FeatureColourChooser(ap.alignFrame, name.getText()); + dialog.transferFocus(); } - index++; } - } + }); + dialog.setVisible(true); - renderOrder = new String[allfeatures.size()]; - Enumeration en = allfeatures.elements(); - int i = allfeatures.size() - 1; - while (en.hasMoreElements()) + FeaturesFile ffile = new FeaturesFile(); + + if (dialog.accept) { - renderOrder[i] = en.nextElement().toString(); - i--; + lastFeatureAdded = name.getText().trim(); + lastFeatureGroupAdded = source.getText().trim(); + lastDescriptionAdded = description.getText().replace('\n', ' '); } - } - public Color getColour(String featureType) - { - return (Color) featureColours.get(featureType); - } - - public void addNewFeature(String name, Color col) - { - - setColour(name, col); - if (av.featuresDisplayed == null) + if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1) { - av.featuresDisplayed = new Hashtable(); + lastFeatureGroupAdded = null; } - av.featuresDisplayed.put(name, "NOGROUP"); - } - - public void setColour(String featureType, Color col) - { - featureColours.put(featureType, col); - } - - public void setFeaturePriority(Object[][] data) - { - // The feature table will display high priority - // features at the top, but theses are the ones - // we need to render last, so invert the data - if (av.featuresDisplayed != null) + if (!newFeatures) { - av.featuresDisplayed.clear(); - } - renderOrder = new String[data.length]; + SequenceFeature sf = features[featureIndex]; + if (dialog.accept) + { + sf.type = lastFeatureAdded; + sf.featureGroup = lastFeatureGroupAdded; + sf.description = lastDescriptionAdded; + if (!colourPanel.isGcol) + { + // update colour - otherwise its already done. + setColour(sf.type, new FeatureColour(colourPanel.getBackground())); + } + try + { + sf.begin = Integer.parseInt(start.getText()); + sf.end = Integer.parseInt(end.getText()); + } catch (NumberFormatException ex) + { + } + + ffile.parseDescriptionHTML(sf, false); + setVisible(lastFeatureAdded); // if user edited name then make sure new + // type is visible + } + if (deleteFeature) + { + sequences[0].deleteFeature(sf); + } - if (data.length > 0) + } + else { - for (int i = 0; i < data.length; i++) + if (dialog.accept && name.getText().length() > 0) { - String type = data[i][0].toString(); - setColour(type, (Color) data[i][1]); - if ( ( (Boolean) data[i][2]).booleanValue()) + for (int i = 0; i < sequences.length; i++) { - av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB())); + features[i].type = lastFeatureAdded; + features[i].featureGroup = lastFeatureGroupAdded; + features[i].description = lastDescriptionAdded; + sequences[i].addSequenceFeature(features[i]); + ffile.parseDescriptionHTML(features[i], false); } - renderOrder[data.length - i - 1] = type; + Color newColour = colourPanel.getBackground(); + // setColour(lastFeatureAdded, fcol); + + if (lastFeatureGroupAdded != null) + { + setGroupVisibility(lastFeatureGroupAdded, true); + } + setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol + setVisible(lastFeatureAdded); + findAllFeatures(false); // different to original applet behaviour ? + // findAllFeatures(); + } + else + { + // no update to the alignment + return false; } } - } + // refresh the alignment and the feature settings dialog + if (((jalview.appletgui.AlignViewport) av).featureSettings != null) + { + ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable(); + } + // findAllFeatures(); - public void featuresAdded() - { - findAllFeatures(); - } -} + ap.paintAlignment(true); -class TransparencySetter -{ - void setTransparency(Graphics g, float value) - { - Graphics2D g2 = (Graphics2D) g; - g2.setComposite( - AlphaComposite.getInstance( - AlphaComposite.SRC_OVER, value)); + return true; } }